Variant report

Variant	rs10992447
Chromosome Location	chr9:95509733-95509734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95500735..95502808-chr9:95507809..95510378,3	MCF-7	breast:
2	chr9:95491392..95494883-chr9:95508865..95510540,3	K562	blood:
3	chr9:95501433..95503464-chr9:95508395..95511050,2	K562	blood:
4	chr9:95504029..95507342-chr9:95507599..95511465,3	MCF-7	breast:
5	chr9:95504668..95516688-chr9:95523327..95528935,18	MCF-7	breast:
6	chr9:95499325..95502717-chr9:95506980..95509904,5	MCF-7	breast:
7	chr9:95507487..95509830-chr9:95526324..95529245,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185963	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1040977	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10820998	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs10821001	0.82[EUR][1000 genomes]
rs10821003	0.82[EUR][1000 genomes]
rs10821004	0.84[EUR][1000 genomes]
rs10821005	0.84[EUR][1000 genomes]
rs10821011	0.83[EUR][1000 genomes]
rs10821014	0.84[EUR][1000 genomes]
rs10992367	0.89[TSI][hapmap]
rs10992380	0.89[TSI][hapmap]
rs10992384	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs10992390	0.84[CEU][hapmap]
rs10992392	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs10992396	0.81[EUR][1000 genomes]
rs10992406	0.91[CEU][hapmap]
rs10992407	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10992408	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10992409	0.81[EUR][1000 genomes]
rs10992412	0.81[EUR][1000 genomes]
rs10992414	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10992416	0.81[EUR][1000 genomes]
rs10992417	0.81[EUR][1000 genomes]
rs10992420	0.82[EUR][1000 genomes]
rs10992422	0.84[EUR][1000 genomes]
rs10992423	0.82[EUR][1000 genomes]
rs10992437	0.82[EUR][1000 genomes]
rs10992448	1.00[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs10992453	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10992460	1.00[CEU][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs10992461	1.00[CEU][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs11533010	0.84[EUR][1000 genomes]
rs12236754	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12238691	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12684587	0.82[EUR][1000 genomes]
rs12685358	0.84[EUR][1000 genomes]
rs12686771	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1323523	0.84[CEU][hapmap]
rs1326775	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs1575460	0.84[CEU][hapmap]
rs16908555	0.92[CEU][hapmap]
rs16908560	0.91[CEU][hapmap]
rs1853428	0.92[CEU][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs1853468	0.84[CEU][hapmap]
rs1974004	0.92[CEU][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs2146848	0.84[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs2148537	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs2181584	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2277169	0.86[EUR][1000 genomes]
rs2398780	0.82[CEU][hapmap]
rs3739605	1.00[CEU][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs56311406	0.82[EUR][1000 genomes]
rs57737182	0.82[EUR][1000 genomes]
rs58952648	0.84[EUR][1000 genomes]
rs60498616	0.84[EUR][1000 genomes]
rs61628776	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7031163	1.00[CEU][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs72756476	0.83[EUR][1000 genomes]
rs753804	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs7850075	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs7856147	0.84[CEU][hapmap]
rs7857105	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs7857502	0.84[CEU][hapmap]
rs7860628	0.82[EUR][1000 genomes]
rs7863741	0.81[EUR][1000 genomes]
rs7869603	0.84[EUR][1000 genomes]
rs7871537	0.84[CEU][hapmap]
rs7875050	0.90[CEU][hapmap]
rs912261	0.92[CEU][hapmap]
rs912264	0.84[CEU][hapmap]
rs971984	0.84[CEU][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10992447	OMD	cis	parietal	SCAN
rs10992447	FBP1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95485600-95511600	Weak transcription	Aorta	Aorta
2	chr9:95498600-95510200	Weak transcription	Hela-S3	cervix
3	chr9:95502000-95511200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:95502200-95511200	Weak transcription	Fetal Brain Male	brain
5	chr9:95502200-95511600	Weak transcription	Fetal Brain Female	brain
6	chr9:95502400-95516400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:95503400-95511600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:95503400-95518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:95503600-95509800	Weak transcription	Fetal Intestine Small	intestine
10	chr9:95503600-95510400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:95503600-95514400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr9:95503600-95514400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:95503600-95517800	Weak transcription	Fetal Intestine Large	intestine
14	chr9:95503800-95523800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:95504400-95509800	Weak transcription	NHEK	skin
16	chr9:95505400-95509800	Weak transcription	GM12878-XiMat	blood
17	chr9:95505400-95510000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr9:95506000-95510400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr9:95507200-95512400	Enhancers	Lung	lung
20	chr9:95507200-95512600	Enhancers	Left Ventricle	heart
21	chr9:95507200-95512600	Enhancers	Ovary	ovary
22	chr9:95507400-95510000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:95507400-95510000	Enhancers	Fetal Muscle Leg	muscle
24	chr9:95507400-95510200	Enhancers	Spleen	Spleen
25	chr9:95507400-95510400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr9:95507400-95510800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr9:95507400-95510800	Enhancers	HUVEC	blood vessel
28	chr9:95507400-95511000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:95507400-95511200	Enhancers	K562	blood
30	chr9:95507400-95511600	Enhancers	Brain Cingulate Gyrus	brain
31	chr9:95507400-95512200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr9:95507400-95512400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:95507400-95512400	Enhancers	Right Atrium	heart
34	chr9:95507400-95512600	Enhancers	Placenta	Placenta
35	chr9:95507400-95512600	Enhancers	Right Ventricle	heart
36	chr9:95507400-95512800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:95507400-95512800	Enhancers	Fetal Heart	heart
38	chr9:95507400-95513200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr9:95507400-95513800	Enhancers	Primary B cells from peripheral blood	blood
40	chr9:95507600-95510400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr9:95507600-95510800	Enhancers	Pancreas	Pancrea
42	chr9:95507600-95512400	Enhancers	Fetal Muscle Trunk	muscle
43	chr9:95507600-95512600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr9:95507800-95511400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr9:95508000-95512200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:95508000-95517800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr9:95508200-95510400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr9:95508200-95512000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:95508200-95512400	Enhancers	NHLF	lung
50	chr9:95508200-95515000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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